4HSU | pdb_00004hsu

Crystal structure of LSD2-NPAC with H3(1-26)in space group P21

PDB DOI: https://doi.org/10.2210/pdb4HSU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens, Xenopus laevis
Expression System: Spodoptera frugiperda, Escherichia coli
Mutation(s): Yes

Deposited: 2012-10-30 Released: 2013-02-13
Deposition Author(s): Chen, F., Dong, Z., Fang, J., Xu, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.232 (Depositor), 0.233 (DCC)
R-Value Work:
0.199 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural insight into substrate recognition by histone demethylase LSD2/KDM1b.

Chen, F., Yang, H., Dong, Z., Fang, J., Wang, P., Zhu, T., Gong, W., Fang, R., Shi, Y.G., Li, Z., Xu, Y.

(2013) Cell Res 23: 306-309

PubMed: 23357850 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/cr.2013.17
Primary Citation Related Structures:
4GU0, 4HSU

Macromolecule Content

Total Structure Weight: 104.74 kDa
Atom Count: 6,505
Modeled Residue Count: 775
Deposited Residue Count: 930
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific histone demethylase 1B	A	776	Homo sapiens	Mutation(s): 0 Gene Names: LSD2 EC: 1 (PDB Primary Data), 1.14.99.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NB78 (Homo sapiens) Explore Q8NB78 Go to UniProtKB: Q8NB78
PHAROS: Q8NB78 GTEx: ENSG00000165097
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NB78
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase GLYR1	B	124	Homo sapiens	Mutation(s): 0 Gene Names: GLYR1 EC: 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q49A26 (Homo sapiens) Explore Q49A26 Go to UniProtKB: Q49A26
PHAROS: Q49A26 GTEx: ENSG00000140632
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q49A26
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	C	30	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for Q92133 (Xenopus laevis) Explore Q92133 Go to UniProtKB: Q92133
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92133
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.232 (Depositor), 0.233 (DCC)
R-Value Work: 0.199 (Depositor), 0.200 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.754	α = 90
b = 89.481	β = 102.89
c = 88.349	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-02-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-02-13
Type: Initial release
Version 1.1: 2013-07-10
Changes: Database references
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description